Structure validation: Difference between revisions

Revision as of 07:34, 29 January 2020

Revision as of 08:58, 29 January 2020

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==Historical summary==

Macromolecular crystallography was preceded by the older field of small-molecule [[x-ray crystallography]] (for structures with less than a few hundred atoms). Small-molecule [[diffraction]] data extends to much higher [[Resolution (electron density)|resolution]] than feasible for macromolecules, and has a very clean mathematical relationship between the data and the atomic model. The residual, or R-factor, measures the agreement between the experimental data and the values back-calculated from the atomic model. For a well-determined small-molecule structure the R-factor is nearly as small as the uncertainty in the experimental data (well under 5%). Therefore, that one test by itself provides most of the validation needed, but a number of additional consistency and methodology checks are done by automated software<ref>{{Cite journal |author vauthors = Spek AL |year=2003 |title=Single-crystal structure validation with the program PLATON |journal=Journal of Applied Crystallography |volume= 36 |pages=7–13 |doi=10.1107/S0021889802022112}}</ref> as a requirement for small-molecule crystal structure papers submitted to the [[International Union of Crystallography]] (IUCr) journals such as [[Acta Crystallographica]] section B or C. Atomic coordinates of these small-molecule structures are archived and accessed through the [[Cambridge Structural Database]] (CSD)<ref>{{Citecite journal |author vauthors = Allen FH |year=2002 |title = The Cambridge Structural Database: a quarter of a million crystal structures and rising | journal = Acta Crystallographica. Section B, Structural Science | volume = 58 | issue = Pt 3 Pt 1 | pages =380–388 380–8 | date = June 2002 | pmid = 12037359 | doi = 10.1107/S0108768102003890 }}</ref> or the [[Crystallography Open Database]] (COD).<ref>{{cite journal | vauthors = Gražulis S, Chateigner D, Downs RT, Yokochi AF, Quirós M, Lutterotti L, Manakova E, Butkus J, Moeck P, Le Bail A | display-authors = 6 | title = Crystallography Open Database - an open-access collection of crystal structures | journal = Journal of Applied Crystallography | volume = 42 | issue = Pt 4 | pages = 726–729 | date = August 2009 | pmid = 22477773 | pmc = 3253730 | doi = 10.1107/s0021889809016690 }}</ref>

The first macromolecular validation software was developed around 1990, for proteins. It included Rfree [[cross-validation (statistics)|cross-validation]] for model-to-data match,<ref name="Rfree">{{cite journal | vauthors = Brünger AT | title = Free R value: a novel statistical quantity for assessing the accuracy of crystal structures | journal = Nature | volume = 355 | issue = 6359 | pages = 472–5 | date = January 1992 | pmid = 18481394 | doi = 10.1038/355472a0 | author-link = Axel T. Brunger | bibcode = 1992Natur.355..472B }}</ref> bond length and angle parameters for covalent geometry,<ref name="Engh">{{cite journal |vauthors=Engh RA, Huber R |year=1991 |title=Accurate bond and angle parameters for X-ray protein structure refinement |journal=Acta Crystallographica A |volume=47 |issue=4 |pages=392&ndash;400|doi=10.1107/s0108767391001071 }}</ref> and sidechain and backbone conformational criteria.<ref name="Ponder&Richards">{{cite journal |vauthors=Ponder JW, Richards FM |year=1987 |title=Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes |journal=Journal of Molecular Biology |volume=193 |issue=4 |pages=775–791 |doi=10.1016/0022-2836(87)90358-5|pmid=2441069 }}</ref><ref name="procheck">{{cite journal |vauthors=Laskowski RA, MacArthur MW, Moss DS, Thornton JM |author4-link=Janet Thornton |year=1993 |title=PROCHECK: a program to check the stereochemical quality of protein structures |journal=Journal of Applied Crystallography |volume=26 |issue=2 |pages=283–291 |doi=10.1107/s0021889892009944}}</ref><ref name="whatif">{{cite journal | vauthors = Hooft RW, Vriend G, Sander C, Abola EE | title = Errors in protein structures | journal = Nature | volume = 381 | issue = 6580 | pages = 272 | date = May 1996 | pmid = 8692262 | doi = 10.1038/381272a0 | bibcode = 1996Natur.381..272H }}</ref> For macromolecular structures, the atomic models are deposited in the [[Protein Data Bank]] (PDB), still the single archive of this data. The PDB was established in the 1970s at [[Brookhaven National Laboratory]],<ref>{{cite journal | vauthors = Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M | display-authors = 6 | title = The Protein Data Bank: a computer-based archival file for macromolecular structures | journal = Journal of Molecular Biology | volume = 112 | issue = 3 | pages = 535–42 | date = May 1977 | pmid = 875032 | doi = 10.1016/s0022-2836(77)80200-3 | author7-link = Olga Kennard }}</ref> moved in 2000 to the [http://www.rcsb.org/pdb RCSB] (Research Collaboration for Structural Biology) centered at [[Rutgers]],<ref>{{cite journal | vauthors = Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE | display-authors = 6 | title = The Protein Data Bank | journal = Nucleic Acids Research | volume = 28 | issue = 1 | pages = 235–42 | date = January 2000 | pmid = 10592235 | pmc = 102472 | doi = 10.1093/nar/28.1.235 | author8-link = Philip Bourne | author-link = Helen M. Berman }}</ref> and expanded in 2003 to become the [http://www.wwpdb.org/ wwPDB] (worldwide Protein Data Bank),<ref name="wwPDB">{{cite journal | vauthors = Berman H, Henrick K, Nakamura H | title = Announcing the worldwide Protein Data Bank | journal = Nature Structural Biology | volume = 10 | issue = 12 | pages = 980 | date = December 2003 | pmid = 14634627 | doi = 10.1038/nsb1203-980 | author-link = Helen M. Berman }}</ref> with access sites added in Europe ([http://pdbe.org|PDBe]) and Asia ([http://www.pdbj.org|PDBj]), and with NMR data handled at the [http://www.bmrb.wisc.edu BioMagResBank (BMRB)] in Wisconsin.

Validation rapidly became standard in the field,<ref name="Kleywegt2000">{{cite journal |author vauthors = Kleywegt GJ |year= 2000 |title= Validation of protein crystal structures |journal=Acta Crystallographica D |volume=56 |pages=18–19}}</ref> with further developments described below. *Obviously needs expansion*

A large boost was given to the applicability of comprehensive validation for both x-ray and NMR as of February 1, 2008, when the worldwide [[Protein Data Bank]] (wwPDB) made mandatory the deposition of experimental data along with atomic coordinates. Since 2012 strong forms of validation have been in the process of being adopted for [http://www.wwpdb.org/validation.html wwPDB deposition] from recommendations of the wwPDB Validation Task Force committees for [[x-ray crystallography]],<ref name="xrayVTF">{{cite journal | vauthors = Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH | display-authors = 6 | title = A new generation of crystallographic validation tools for the protein data bank | journal = Structure | volume = 19 | issue = 10 | pages = 1395–412 | date = October 2011 | pmid = 22000512 | pmc = 3195755 | doi = 10.1016/j.str.2011.08.006 | author12-link = Jane Richardson (chemist) | author7-link = Gerard Kleywegt | author4-link = Axel Brunger }}</ref> for NMR,<ref name="nmrVTF">{{cite journal | vauthors = Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL | display-authors = 6 | title = Recommendations of the wwPDB NMR Validation Task Force | journal = Structure | volume = 21 | issue = 9 | pages = 1563–70 | date = September 2013 | pmid = 24010715 | pmc = 3884077 | doi = 10.1016/j.str.2013.07.021 | author12-link = Gerard Kleywegt | author11-link = Helen M. Berman | author3-link = Ad Bax | author6-link = Jane Richardson (chemist) }}</ref> for SAXS ([[SAXS|small-angle x-ray scattering]]), and for cryoEM (cryo-[[Electron Microscopy]]).<ref name="emVTF">{{cite journal | vauthors = Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL | display-authors = 6 | title = Outcome of the first electron microscopy validation task force meeting | journal = Structure | volume = 20 | issue = 2 | pages = 205–14 | date = February 2012 | pmid = 22325770 | pmc = 3328769 | doi = 10.1016/j.str.2011.12.014 | author16-link = Michael Rossmann | author-link = Richard Henderson (biologist) }}</ref>

== Stages of validation ==

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====Geometry====

<ref name="Engh" /><ref name="Gelbin">{{cite journal |vauthors=Gelbin A, Schneider B, Clowney L, ((Hsieh S-H)), Olson WK, Berman HM |author6-link=Helen M. Berman |year=1996 |title=Geometric parameters in Nucleic Acids:Sugar and Phosphate Constituents |journal=Journal of the American Chemical Society |volume=118 |issue=3 |pages=519–529 |doi=10.1021/ja9528846}}</ref><ref>{{cite journal | vauthors = Schultze P, Feigon J | title = Chirality errors in nucleic acid structures | journal = Nature | volume = 387 | issue = 6634 | pages = 668 | date = June 1997 | pmid = 9192890 | doi = 10.1038/42632 | bibcode = 1997Natur.387..668S }}</ref>

====Conformation (dihedrals): protein & RNA====

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====Packing and Electrostatics ====

For globular proteins, interior atomic packing (arising from short-range, local interactions) of side-chains<ref>{{Cite journal|last vauthors = Shen|first=Min-yi|last2= MY, Davis|first2=Fred P.|last3=FP, Sali|first3=Andrej A |date= March 2005-03|title=The optimal size of a globular protein ___domain: A simple sphere-packing model|url=http://dx.doi.org/10.1016/j.cplett.2005.02.029|journal=Chemical Physics Letters|volume=405|issue=1-31–3|pages=224–228|doi=10.1016/j.cplett.2005.02.029|issn=0009-2614|bibcode= 2005CPL...405..224S}}</ref><ref>{{Citecite journal |last vauthors = Misura|first=Kira M.S.|last2=KM, Morozov|first2=Alexandre V.|last3=AV, Baker D |first3=David|date=2004-09| title = Analysis of Anisotropicanisotropic Sideside-chain Packingpacking in Proteinsproteins and Applicationapplication to Highhigh-resolution Structurestructure prediction Prediction|url=http://dx.doi.org/10.1016/j.jmb.2004.07.038| journal = Journal of Molecular Biology | volume = 342 | issue = 2 | pages =651–664 651–64 | date = September 2004 | pmid = 15327962 | doi = 10.1016/j.jmb.2004.07.038|issn=0022-2836 }}</ref><ref>{{Citecite journal |last vauthors = Basu|first=Sankar|last2= S, Bhattacharyya|first2=Dhananjay|last3= D, Banerjee R |first3=Rahul|date=2011-05-24| title = Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs |url=https://doi.org/10.1186/1471-2105-12-195| journal = BMC Bioinformatics |language=en| volume = 12 | issue = 1 | pages = 195 | date = May 2011 | pmid = 21605466 | pmc = 3123238 | doi = 10.1186/1471-2105-12-195|issn=1471-2105|pmc=PMC3123238|pmid=21605466 }}</ref><ref>{{Citecite journal |last vauthors = Banerjee|first=Rahul|last2= R, Sen|first2=Malabika|last3= M, Bhattacharya|first3=Dhananjay|last4= D, Saha P |first4=Partha|date=2003-10-10| title = The jigsaw puzzle model: search for conformational specificity in protein interiors |url=https://www.ncbi.nlm.nih.gov/pubmed/14516754| journal = Journal of Molecular Biology | volume = 333 | issue = 1 | pages =211–226 211–26 | date = October 2003 | pmid = 14516754 | doi = 10.1016/j.jmb.2003.08.013|issn=0022-2836|pmid=14516754 }}</ref> has been shown to be pivotal in the structural stabilization of the protein-fold. On the other hand, the electrostatic harmony (non-local, long-range) of the overall fold<ref name=":2">{{Citecite journal |last vauthors = Basu|first=Sankar|last2= S, Bhattacharyya|first2=Dhananjay|last3= D, Banerjee R |first3=Rahul|date=2012-06-06| title = Self-Complementaritycomplementarity within Proteinsproteins: Bridgingbridging the Gapgap between Bindingbinding and Folding|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368132/folding | journal = Biophysical Journal | volume = 102 | issue = 11 | pages =2605–2614 2605–14 | date = June 2012 | pmid = 22713576 | pmc = 3368132 | doi = 10.1016/j.bpj.2012.04.029 |issn bibcode =0006-3495|pmc=3368132|pmid=22713576 2012BpJ...102.2605B }}</ref> has also been shown to be essential for its stabilization. Packing anomalies include steric clashes<ref>{{Citecite journal |last vauthors = Chen|first=Vincent B.|last2=VB, Arendall|first2=W. Bryan|last3=WB, Headd|first3=Jeffrey J.|last4=JJ, Keedy|first4=Daniel A.|last5=DA, Immormino|first5=Robert M.|last6=RM, Kapral|first6=Gary J.|last7=GJ, Murray|first7=Laura W.|last8=LW, Richardson|first8=Jane S.|last9=JS, Richardson DC |first9 display-authors =David C.|date=2010-01-016 | title = MolProbity: all-atom structure validation for macromolecular crystallography |url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803126/| journal = Acta Crystallographica. Section D:, Biological Crystallography | volume = 66 | issue = Pt 1 | pages = 12–21 |doi date =10.1107/S0907444909042073 January 2010 |issn pmid =0907-4449 20057044 | pmc = 2803126 |pmid doi =20057044 10.1107/S0907444909042073 }}</ref>, short contacts<ref>{{Citecite journal |last vauthors = Banerjee|first=Rahul|last2= R, Sen|first2=Malabika|last3= M, Bhattacharya|first3=Dhananjay|last4= D, Saha P |first4=Partha|date=2003-10-10| title = The jigsaw puzzle model: search for conformational specificity in protein interiors |url=https://www.ncbi.nlm.nih.gov/pubmed/14516754| journal = Journal of Molecular Biology | volume = 333 | issue = 1 | pages =211–226 211–26 | date = October 2003 | pmid = 14516754 | doi = 10.1016/j.jmb.2003.08.013|issn=0022-2836|pmid=14516754 }}</ref>, holes<ref>{{Citecite journal |last vauthors = Sheffler|first=Will|last2= W, Baker D |first2=David|date=2008| title = RosettaHoles: Rapidrapid assessment of protein core packing for structure prediction, refinement, design, and validation |url=http://dx.doi.org/10.1002/pro.8| journal = Protein Science | volume = 18 | issue = 1 | pages =NA–NA 229–39 | date = January 2009 | pmid = 19177366 | pmc = 2708028 | doi = 10.1002/pro.8|issn=0961-8368 }}</ref> and cavities<ref>{{Citecite journal |last vauthors = Chakravarty|first= S.|last2=, Varadarajan|first2= R.|date=1999-07-15 | title = Residue depth: a novel parameter for the analysis of protein structure and stability |url=https://www.ncbi.nlm.nih.gov/pubmed/10425675| journal = Structure (London, England: 1993)| volume = 7 | issue = 7 | pages =723–732 723–32 | date = July 1999 | pmid = 10425675 | doi = 10.1016/s0969-2126(99)80097-5|issn=0969-2126|pmid=10425675 }}</ref> while electrostatic disharmony<ref name=":2" /><ref>{{Citecite journal |last vauthors = Basu|first=Sankar|last2= S, Bhattacharyya|first2=Dhananjay|last3= D, Banerjee R |first3=Rahul|date=2014-06| title = Applications of complementarity plot in error detection and structure validation of proteins |url=https://www.ncbi.nlm.nih.gov/pubmed/25204080| journal = Indian Journal of Biochemistry & Biophysics | volume = 51 | issue = 3 | pages = 188–200 |issn date =0301-1208 June 2014 | pmid = 25204080 }}</ref> refer to unbalanced partial charges in the protein core (particularly relevant for designed protein interiors). While the clash-score of [http://molprobity.biochem.duke.edu/ Molprobity] identifies steric clashes at a very high resolution, the [[Complementarity plot|Complementarity Plot]] combines packing anomalies with electrostatic imbalance of side-chains and signals for either or both.

<br />

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[[File:(A)-ASN297.svg|thumb|A 2D diagram of an N-glycan linked to an antibody fragment in the structure with PDB accession code '4BYH'. This diagram, which has been generated with Privateer,<ref name=":0"/> follows the standard symbol nomenclature<ref name=":1"/> and includes, in its original svg format, annotations containing validation information, including ring conformation and detected monosaccharide types.]]

The branched and cyclic nature of carbohydrates poses particular problems to structure validation tools.<ref>{{cite journal | vauthors = Agirre J, Davies GJ, Wilson KS, Cowtan KD | title = Carbohydrate structure: the rocky road to automation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 39–47 | date = June 2017 | pmid = 27940408 | doi = 10.1016/j.sbi.2016.11.011 | series = Carbohydrates • Sequences and topology | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf | series = Carbohydrates • Sequences and topology }}</ref> At higher resolutions, it is possible to determine the sequence/structure of oligo- and poly-saccharides, both as covalent modifications and as ligands. However, at lower resolutions (typically lower than 2.0Å), sequences/structures should either match known structures, or be supported by complementary techniques such as Mass Spectrometry.<ref>{{cite journal | vauthors = Crispin M, Stuart DI, Jones EY | title = Building meaningful models of glycoproteins | journal = Nature Structural & Molecular Biology | volume = 14 | issue = 5 | pages = 354; discussion 354-5354–5 | date = May 2007 | pmid = 17473875 | doi = 10.1038/nsmb0507-354a }}</ref> Also, monosaccharides have clear conformational preferences (saturated rings are typically found in chair conformations),<ref>{{cite journal | vauthors = Davies GJ, Planas A, Rovira C | title = Conformational analyses of the reaction coordinate of glycosidases | journal = Accounts of Chemical Research | volume = 45 | issue = 2 | pages = 308–16 | date = February 2012 | pmid = 21923088 | doi = 10.1021/ar2001765 }}</ref> but errors introduced during model building and/or refinement (wrong linkage chirality or distance, or wrong choice of model - see<ref>{{cite journal | vauthors = Agirre J | title = Strategies for carbohydrate model building, refinement and validation | journal = Acta Crystallographica. Section D, Structural Biology | volume = 73 | issue = Pt 2 | pages = 171–186 | date = February 2017 | pmid = 28177313 | pmc = 5297920 | doi = 10.1107/S2059798316016910 | url = http://journals.iucr.org/d/issues/2017/02/00/ba5257/ }}</ref> for recommendations on carbohydrate model building and refinement and<ref>{{cite journal | vauthors = Lütteke T | title = Analysis and validation of carbohydrate three-dimensional structures | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 65 | issue = Pt 2 | pages = 156–68 | date = February 2009 | pmid = 19171971 | pmc = 2631634 | doi = 10.1107/S0907444909001905 }}</ref><ref>{{Citecite journal book|last vauthors = Lütteke|first=Thomas|last2= T, von der Lieth|first2=Claus W.|date=2009-01-01CW | title = Data mining the PDB for glyco-related data | journal = Methods in Molecular Biology | volume = 534 | pages = 293–310 | date = 2009-01-01 | pmid = 19277543 | doi = 10.1007/978-1-59745-022-5_21 |pmid=19277543| isbn = 978-1-58829-774-7 }}</ref><ref>{{cite journal | vauthors = Joosten RP, Lütteke T | title = Carbohydrate 3D structure validation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 9–17 | date = June 2017 | pmid = 27816840 | doi = 10.1016/j.sbi.2016.10.010 | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf }}</ref> for reviews on general errors in carbohydrate structures) can bring their atomic models out of their energy minima. Around 20% of the deposited carbohydrate structures are in unjustified energy minima.<ref>{{cite journal | vauthors = Agirre J, Davies G, Wilson K, Cowtan K | title = Carbohydrate anomalies in the PDB | journal = Nature Chemical Biology | volume = 11 | issue = 5 | pages = 303 | date = May 2015 | pmid = 25885951 | doi = 10.1038/nchembio.1798 }}</ref>

A number of carbohydrate validation web services are available at [http://ww.glycosciences.de glycosciences.de] (including nomenclature checks and linkage checks by [http://www.glycosciences.de/tools/pdb-care/ pdb-care],<ref>{{cite journal | vauthors = Lütteke T, von der Lieth CW | title = pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files | journal = BMC Bioinformatics | volume = 5 | pages = 69 | date = June 2004 | pmid = 15180909 | pmc = 441419 | doi = 10.1186/1471-2105-5-69 }}</ref> and cross-validation with Mass Spectrometry data through the use of GlycanBuilder), whereas the [http://www.ccp4.ac.uk CCP4] suite currently distributes [http://www.ccp4.ac.uk/html/privateer.html Privateer],<ref name=":0">{{cite journal | vauthors = Agirre J, Iglesias-Fernández J, Rovira C, Davies GJ, Wilson KS, Cowtan KD | title = Privateer: software for the conformational validation of carbohydrate structures | journal = Nature Structural & Molecular Biology | volume = 22 | issue = 11 | pages = 833–4 | date = November 2015 | pmid = 26581513 | doi = 10.1038/nsmb.3115 }}</ref> which is a tool that is integrated into the model building and refinement process itself. Privateer is able to check stereo- and regio-chemistry, ring conformation and puckering, linkage torsions, and real-space correlation against positive omit density, generating aperiodic torsion restraints on ring bonds, which can be used by any refinement software in order to maintain the monosaccharide's minimal energy conformation.<ref name=":0" />

Privateer also generates scalable two-dimensional SVG diagrams according to the Essentials of Glycobiology<ref name=":1">{{cite journal | vauthors = Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T, Prestegard JJ, Schnaar RL, Freeze HH, Marth JD, Bertozzi CR, Etzler ME, Frank M, Vliegenthart JF, Lütteke T, Perez S, Bolton E, Rudd P, Paulson J, Kanehisa M, Toukach P, Aoki-Kinoshita KF, Dell A, Narimatsu H, York W, Taniguchi N, Kornfeld S | display-authors = 6 | title = Symbol Nomenclature for Graphical Representations of Glycans | journal = Glycobiology | volume = 25 | issue = 12 | pages = 1323–4 | date = December 2015 | pmid = 26543186 | pmc = 4643639 | doi = 10.1093/glycob/cwv091 }}</ref> standard symbol nomenclature containing all the validation information as tooltip annotations (see figure). This functionality is currently integrated into other CCP4 programs, such as the molecular graphics program CCP4mg (through the ''Glycoblocks'' 3D representation,<ref>{{cite journal | vauthors = McNicholas S, Agirre J | title = Glycoblocks: a schematic three-dimensional representation for glycans and their interactions | journal = Acta Crystallographica. Section D, Structural Biology | volume = 73 | issue = Pt 2 | pages = 187–194 | date = February 2017 | pmid = 28177314 | pmc = 5297921 | doi = 10.1107/S2059798316013553 }}</ref> which conforms to the standard symbol nomenclature<ref name=":1" />) and the suite's graphical interface, CCP4i2.

==Validation for crystallography==

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== In SAXS ==

SAXS (small-angle x-ray scattering) is a rapidly growing area of structure determination, both as a source of approximate 3D structure for initial or difficult cases and as a component of hybrid-method structure determination when combined with NMR, EM, crystallographic, cross-linking, or computational information. There is great interest in the development of reliable validation standards for SAXS data interpretation and for quality of the resulting models, but there are as yet no established methods in general use. Three recent steps in this direction are the creation of a Small-Angle Scattering Validation Task Force committee by the worldwide Protein DataBank and its initial report,<ref name="sasVTF">{{cite journal | vauthors = Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM | display-authors = 6 | title = Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB | journal = Structure | volume = 21 | issue = 6 | pages = 875–81 | date = June 2013 | pmid = 23747111 | doi = 10.1016/j.str.2013.04.020 }}</ref> a set of suggested standards for data inclusion in publications,<ref name="Jacques2012">{{cite journal | vauthors = Jacques DA, Guss JM, Svergun DI, Trewhella J | title = Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 68 | issue = Pt 6 | pages = 620–6 | date = June 2012 | pmid = 22683784 | doi = 10.1107/S0907444912012073 }}</ref> and an initial proposal of statistically derived criteria for automated quality evaluation.<ref name="Grant2015">{{cite journal | vauthors = Grant TD, Luft JR, Carter LG, Matsui T, Weiss TM, Martel A, Snell EH | title = The accurate assessment of small-angle X-ray scattering data | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 71 | issue = Pt 1 | pages = 45–56 | date = January 2015 | pmid = 25615859 | pmc = 4304685 | doi = 10.1107/S1399004714010876 }}</ref>

==For computational biology==

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== Further reading ==

{{Refbegin}}

*{{Cite book |author last1 = Cavanagh, | first1 = John |author2 last2 = Fairbrother, | first2 = Wayne J. |author3 last3 = Palmer, | first3 = Arthur G. III |author4 last4 = Skelton, | first4 = Nicholas J. | name-list-format = vanc |title=Protein NMR Spectroscopy: Principles and Practice |edition=2nd |year=2006 |publisher=Academic Press |isbn=978-0-12-164491-8 |ref={{harvid|Cavanagh|2006}} }}

*{{Cite book |last= Rupp |first=Bernhard |title=Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology |year=2009 |publisher=Garland Science |isbn=978-0815340812 |ref=harv}}

{{Refend}}